Background: We reported previously (Kuai et al., NN2005) that perceptual learning of contrast and motion direction discrimination occurs when multi-stimuli are presented in a fixed sequence (temporal patterning), but not randomly (roving), which points to the need for proper stimulus coding for multi-stimulus learning to occur. In this study we examined the stimulus coding rules for perceptual learning with multi-stimuli. Methods: Subjects practice contrast discrimination of Gabors at multiple reference contrasts and orientation discrimination of illusory lines at multiple reference orientations in various roving and temporal pattering conditions. Results: 1) Stimulus rhythm, especially temporally evenly spaced, is necessary for temporal patterning to take effect during practice. 2) Both the encoding phase, and the slow consolidation phases as least 4 hours after each practice session, of perceptual learning are subject to roving disruption; 3) However, after completion of temporal patterned learning, performance is undisrupted by extended roving training, and instead learning is transferable to the roving condition; 4) Roving is ineffective if each stimulus is presented in a block of five or more consecutive trials; 5) Roving is also ineffective if each stimulus has a distinct identity, either due to large inter-stimulus difference, or inherited identity (i.e., cardinal/oblique orientations), or assigned identity through pre-trial letter cueing. Conclusions: Our results sketched some basic rules for stimulus encoding, consolidation, and retrieval for multi-stimulus perceptual learning. These rules may be needed because the brain needs to “tag” each stimulus, in order to switch attention to the appropriate perceptual template. Stimulus temporal patterning assists in tagging stimuli and switching attention through its rhythmic stimulus sequence. However, once the identities are learned, stimulus information can be efficiently retrieved to guide visual discrimination regardless of the stimulus temporal context.